| TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. Journal of Chemical Information and Modeling. American Chemical Society, 2022, vol. 62, No 3, p. 567-576. ISSN 1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651. |
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@article{1839946,
author = {Trapl, Dalibor and Krupička, MArtin and Višňovský, Vladimír and Hozzová, Jana and Oľha, Jaroslav and Křenek, Aleš and Spiwok, Vojtěch},
article_number = {3},
doi = {http://dx.doi.org/10.1021/acs.jcim.1c00651},
keywords = {collective variable; biased potential; force field},
language = {eng},
issn = {1549-9596},
journal = {Journal of Chemical Information and Modeling},
title = {Property Map Collective Variable as a Useful Tool for a Force Field Correction},
url = {https://doi.org/10.1021/acs.jcim.1c00651},
volume = {62},
year = {2022}
}
TY - JOUR
ID - 1839946
AU - Trapl, Dalibor - Krupička, MArtin - Višňovský, Vladimír - Hozzová, Jana - Oľha, Jaroslav - Křenek, Aleš - Spiwok, Vojtěch
PY - 2022
TI - Property Map Collective Variable as a Useful Tool for a Force Field Correction
JF - Journal of Chemical Information and Modeling
VL - 62
IS - 3
SP - 567-576
EP - 567-576
PB - American Chemical Society
SN - 15499596
KW - collective variable
KW - biased potential
KW - force field
UR - https://doi.org/10.1021/acs.jcim.1c00651
N2 - The accuracy of biomolecular simulations depends on the accuracy of an empirical molecular mechanics potential known as a force field: a set of parameters and expressions to estimate the potential from atomic coordinates. Accurate parametrization of force fields for small organic molecules is a challenge due to their high diversity. One of the possible approaches is to apply a correction to the existing force fields. Here, we propose an approach to estimate the density functional theory (DFT)-derived force field correction which is calculated during the run of molecular dynamics without significantly affecting its speed. Using the formula known as a property map collective variable, we approximate the force field correction by a weighted average of this force field correction calculated only for a small series of reference structures. To validate this method, we used seven AMBER force fields, and we show how it is possible to convert one force field to behave like the other one. We also present the force field correction for the important anticancer drug Imatinib as a use case example. Our method appears to be suitable for adjusting the force field for general drug-like molecules. We provide a pipeline that generates the correction; this pipeline is available at https://pmcvff-correction.cerit-sc.cz/.
ER -
TRAPL, Dalibor, MArtin KRUPIČKA, Vladimír VIŠŇOVSKÝ, Jana HOZZOVÁ, Jaroslav OĽHA, Aleš KŘENEK and Vojtěch SPIWOK. Property Map Collective Variable as a Useful Tool for a Force Field Correction. \textit{Journal of Chemical Information and Modeling}. American Chemical Society, 2022, vol.~62, No~3, p.~567-576. ISSN~1549-9596. Available from: https://dx.doi.org/10.1021/acs.jcim.1c00651.
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